The book's witches, described as "demons in human form" are revealed in the opening chapters to be a constant threat to global security. While they look human, and look and act like normal human women, they are secretly plotting to kill every single child on Earth. No other reason for this is given, other than the foul stench children produce for witches.

A young boy (whose name is never mentioned) goes to stay with his (also unnamed) grandmother after his parents are killed in a tragic car crash in the Norwegian mountains when they are on vacation. The boy is comforted by his grandmother, and then she says she will adopt him. The next night, she begins to warn him about witches, which she says are demons in human form, which seek to kill human children. The boy thinks she is bluffing, but she tells him the signs of how to recognize a witch, which include: hair which looks like a wig, because the witches, despite being female, are actually bald, and have to wear wigs to look human; gloves, because the witches actually have inch-long claws which they hide under gloves; inhuman eyes, because the eyes of a witch have a red-white glow; blue spit; and toeless feet, which force the witches to squeeze their feet into pretty tight women's shoes which causes them to limp very slightly. The grandmother also tells the boy that four of her childhood friends were taken and killed by witches, but one girl survived for a while because the witches only managed to turn her into a chicken. Another boy was turned into a porpoise and swam out to sea.

The boy and his grandmother return to England, as per his parents' will. The grandmother warns the boy to be on his guard, since English witches are known to be among the cruellest in the world. Shortly afterward, the boy is building the roof on his treehouse and spots a strange woman in black staring up at him with an eerie smile. When he sees that she is wearing gloves, he instantly recognizes her as a witch; and he also notices her inhuman lips and teeth; her gums resemble "raw meat." When the witch offers him a snake to entice him, he climbs up the tree which he is in and stays there until his grandmother comes and gets him for supper. This persuades the boy and his grandmother to be wary. The boy then becomes conscious of all women he encounters in public and studies them from a distance to check whether they are witches or not.

When the grandmother later becomes ill with pneumonia, the doctor orders her to cancel a planned holiday in Norway. Instead, they go to a luxury hotel in Bournemouth on the southern English coast. The boy goes to train his pet mice in the hotel ballroom when the members of the "Royal Society for the Prevention of Cruelty to Children" show up for their annual meeting. The boy notices one of the women reaching under her hair (with a gloved hand) to scratch at her scalp, and instantly realizes that the "RSPCC" is really the yearly convention of England's witches. A young woman shows up on stage, and removes her face mask to reveal a hideously deformed face underneath. The boy instantly recognizes her as the Grand High Witch. On her cue, the witches reveal their true, demonic forms: bald heads, clawed hands and toeless feet. The Grand High Witch was angry at her English minions' failure to destroy all of the country's children, and orders all of them exterminated by the end of the year. One brave or foolish witch states the obvious; that killing every child in the country is impossible; and the Grand High Witch instantly incinerates her using lasers which shoot from her eyes. The terrified witches do not dare to protest further.

To help them along, she unveils a master plan calling for the witches to purchase sweet shops (with "homemade" money given to them by the Grand High Witch by her money-making machine) and give away free chocolate (for the grand opening) laced with Formula 86 Delayed-Action Mouse Maker, a potion which will change anyone who eats it into a mouse at a specific time. The witches are instructed by the Grand High Witch to set the formula to activate at nine a.m. the day after the children have eaten the chocolate, when they are at school. The teachers, she hopes, will panic and kill the mice, thereby doing the witches' work for them. She warns her followers to only put one dose on each bit of candy that they sell. An overdose could break the delay barrier and even cause a child (especially an adult) to turn into a mouse instantly.

The Grand High Witch turns a gluttonous child named Bruno Jenkins (lured to the convention hall by the promise of free chocolate) into a mouse as a demonstration of her potion. The witches hurriedly put on their disguises as Bruno arrives. At precisely three thirty p.m., Bruno turns into a mouse. Shortly after, the witches smell the narrator's presence, forcing him to make a break for it. He is quickly captured by the witches and turned into a mouse immediately with an overdose of the formula which has the effect of instantly turning him into a mouse.

The formula turns out to have a lucky change: the transformed child retains his or her sentience, personality and even his or her voice. After tracking down Bruno, the transformed boy returns to his grandmother's hotel room and tells her what he has learned. He suggests turning the tables on the witches by slipping Formula 86 into their food. With some difficulty, he manages to get his hands on a bottle of the potion from the Grand High Witch's room. After a failed attempt to return Bruno to his parents, the grandmother takes Bruno and the narrator to dinner in her handbag, whereupon after ordering her meal she slips the narrator onto the floor, allowing him to run to the kitchen. He espies the witches coming in to dinner on his way and enters the kitchen, where he pours the potion into the soup intended for the witches' dinner. The witches all turn into mice within a few minutes, having had massive overdoses. The hotel staff panic and, unknowingly, end up killing all of England's witches. The boy and his grandmother then concoct a plan to destroy all of the world's witches. Learning the location of the witches castle from the hotel's records, they will travel to the Grand High Witch's Norwegian castle (having stolen her notebook), use the potion to change her successor and retainers into mice, then release cats into the castle to kill them. Using the Grand High Witch's money-making machine and information on the whereabouts of all of the world's witches, they will repeat the process all over the world. The grandmother also reveals that as a mouse, the boy will probably only live about another nine years, but the boy doesn't mind it, because he doesn't want to live any longer than his grandmother.